Hi Kevin,
You can do an instrument response in the usual way but you need a high resolution spectrum to compare with so you can match profile including the line. You can see an example of that about halfway down on Christian Buil’s page on reducing LHIRES spectra here
http://www.astrosurf.com/buil/isis/guide_lhires/tuto1_en.htm
and also specifically covered on this page
http://www.astrosurf.com/aras/tutorial5/note1_us.htm
Fortunately unless you are working at the far blue end, atmospheric extinction does not have much effect over the narrow wavelength range so you can use stars which might be some distance from the target (or even at a pinch instrument responses taken on different nights)
Two good sources for high resolution spectra of bright stars are the UVES bright stars
http://www.eso.org/sci/observing/tools/uvespop/bright_stars_uptonow.html
and provided you are working above 4000A,the ELODIE 3.1 list (spectra from the ELODIE archive selected for quality.) See here on ARAS for more background on this set of stars
http://www.spectro-aras.com/forum/viewtopic.php?f=8&t=1369
Both of these are available in the built in ISIS database (you have to load the ELODIE 3.1 star list)
http://www.spectro-aras.com/forum/viewtopic.php?f=8&t=1864
Is it necessary/worth it rather than just rectifying the spectrum for small wavelength ranges? Possibly not, it depends on the application but BeSS recommends it.
Cheers
Robin